FLAMEChooseOptimalClusterNumber
Determine the optimal number of clusters for each sample based on the range of cluster numbers provided to FLAMEMixtureModel.
Version: 4

FLAME

* Public Server Only

FLAMEContourDataGenerator
Generate data which allows the FLAMEViewer to draw a 3-D contour plot of the clusters in the sample.
Version: 1

FLAME

* Public Server Only

FLAMEContourViewer.Pipeline
Run the FLAMEContourDataGenerator and FLAMEViewer modules. Using the pipeline is more convenient than running the two modules individually.
Version: 1

pipeline

* Public Server Only

FLAMEMetacluster
Take the data samples, which have been optimally clustered into subpopulations, and match the subpopulations so that a given population can be identified uniformly across all samples.
Version: 4

SuggestNumberOfPopulationsFCS
The FlowClust module requires that you specify how many populations you are looking for. This module takes a data driven approach and attempts to discover how many populations are present in an FCS file
Version: 1

CreateSymlinks
Creates symlinks to the input files in the job results directory. This is intended to be a helper module for creating scatter-gather pipelines. Note that this module is not supported on Windows
Version: 1

GenePatternDocumentExtractor
Extracts GenePattern pipelines and other embedded GenePattern data from Word 2007 documents created with the Microsoft Word Add-In for the GenePattern Reproducible Research Document.
Version: 1

IlluminaExpressionFileCreator
Creates a GCT file from a zip of Illumina IDAT files and an Illumina manifest file
Version: 2

Preprocess & Utilities

Module Repository

ImputeMissingValues.KNN
Imputes missing values
Version: 13

Missing Value Imputation

Module Repository

ImputeMissingValuesKNN
Imputes missing values
Version: 13

Missing Value Imputation

Module Repository

JavaTreeView
Hierarchical clustering viewer that reads in Eisen's cdt, atr, and gtr files. A detailed description of these formats is available from http\://microarray.ccgb.umn.edu/smd/html/MicroArray/help/formats.shtml
Version: 2

RenameFile
Creates a result file with the contents of the input but with a new name. Where possible, this is done without copying the file but instead by simply making a link. While it is possible to run this with a submitted file, the common use will be to change the name of a result file or a previously uploaded file. Note that the original file will still be present in its original location.
Version: 1

Preprocess & Utilities

Module Repository

ReorderByClass
Reorder the samples in an expression dataset and class file by class
Version: 3